Bryophyte Diversity Patterns Across Biomes in North and South America

Biomes in North and South America

BiomeMap <- qtm(biomes_shp,
                        fill="biomes", 
                        fill.style="fixed",
                        fill.labels=biomes_shp$biomes,
                        fill.palette=cols7,
                        fill.title="Biomes",
                        layout.legend.position=c("left","bottom"),
                        layout.legend.width=1.5,
                        layout.frame=FALSE)
BiomeMap

Figure 1. Map of North and South American biomes.

Beta Diversity Plots by Biome

BiomeBetaWeightBV <- ggplot(BiomeBetaCellsCentCov, aes(x=Type, y=Beta, fill=Type, color=Type)) + 
  geom_boxplot(show.legend = FALSE, fill=biome_cols_11, color="black") +
  guides(x = guide_axis(angle=30)) +
  #theme_minimal() +        #un-comment whichever theme you want
  theme_gray() +
  #theme_light() +
  #theme_bw() +
  geom_violin(scale="count", show.legend=FALSE, fill="gray", alpha=0.35,
              color="gray25") +
  xlab("Biome") +
  ylab("Beta Diversity") +  
  theme(axis.title.y = element_text(size=22), 
        axis.title.x = element_text(size=22),
        axis.text.y = element_text(size=16), 
        axis.text.x = element_text(angle = 30, hjust = 1, size = 16))
BiomeBetaWeightBV

Range Size Plots by Biome

BiomeBetaWeightBV <- ggplot(BiomeBetaCellsCentCov, aes(x=Type, y=Beta, fill=Type, color=Type)) + 
  geom_boxplot(show.legend = FALSE, fill=biome_cols_11, color="black") +
  guides(x = guide_axis(angle=30)) +
  #theme_minimal() +        #un-comment whichever theme you want
  theme_gray() +
  #theme_light() +
  #theme_bw() +
  geom_violin(scale="count", show.legend=FALSE, fill="gray", alpha=0.35,
              color="gray25") +
  xlab("Biome") +
  ylab("Beta Diversity") +  
  theme(axis.title.y = element_text(size=32), 
        axis.title.x = element_text(size=32),
        axis.text.y = element_text(size=16), 
        axis.text.x = element_text(angle = 30, hjust = 1, size = 16))
BiomeBetaWeightBV

Alpha Diversity by Order, Split into Biomes

Orders with Maximum Alpha Diversity > 10

BiomeRangeBV <- ggplot(BiomeRange, aes(x=Type, y=Range, fill=Type, color=Type)) + 
  geom_boxplot(show.legend = FALSE, fill=biome_cols_11, color="black") +
  guides(x = guide_axis(angle=30)) +
  #un-comment whichever theme you want
  #theme_minimal() +        
  theme_gray() +
  #theme_light() +
  #theme_bw() +
  geom_violin(scale="count", show.legend=FALSE, fill="gray", alpha=0.35,
              color="gray25") +
  xlab("Biome") +
  ylab("Range") +  
  theme(axis.title.y = element_text(size=32), 
        axis.title.x = element_text(size=32),
        axis.text.y = element_text(size=20), 
        axis.text.x = element_text(angle = 30, hjust = 1, size = 16))
BiomeRangeBV

Orders with Maximum Alpha Diversity between 10 and 25

FacetOBRBelow10 <- ggplot(OBRBelow10DF, aes(x=Biome, y=Alpha, fill=Biome, color=Biome)) + 
  geom_boxplot(show.legend = FALSE, fill=biome_cols_166, color="black", outlier.size=0.7) +
  #un-comment whichever theme you want
  #theme_minimal() +
  theme_gray() +
  #theme_light() +
  #theme_bw() +
  #theme_dark() +
  #theme_linedraw() +
  #geom_violin(scale="count", show.legend=FALSE, fill="gray", alpha=0.35, color="gray25") +
  xlab("Biome") +
  ylab("Richness") +  
  theme(axis.title.y = element_text(size=32), 
        axis.title.x = element_text(size=32),
        axis.text.y = element_text(size=15), 
        axis.text.x = element_text(angle = 90, hjust = 1, size = 12))+
  facet_wrap(~Order,
             #un-comment # of rows you want
             ncol=6 
             #ncol=5
             )
FacetOBRBelow10

Orders with Maximum Alpha Diversity between 25 and 100

FacetOBR10to25 <- ggplot(OBR10to25DF, aes(x=Biome, y=Alpha, fill=Biome, color=Biome)) + 
  geom_boxplot(show.legend = FALSE, fill=biome_cols_66, color="black", outlier.size=0.7) +
  #un-comment whichever theme you want
  #theme_minimal() +
  theme_gray() +
  #theme_light() +
  #theme_bw() +
  #theme_dark() +
  #theme_linedraw() +
  geom_violin(scale="count", show.legend=FALSE, fill="gray", alpha=0.35, color="gray25") +
  xlab("Biome") +
  ylab("Richness") +  
  theme(axis.title.y = element_text(size=32), 
        axis.title.x = element_text(size=32),
        axis.text.y = element_text(size=15), 
        axis.text.x = element_text(angle = 45, hjust = 1, size = 12))+
  facet_wrap(~Order,
             #un-comment # of rows you want
             ncol=3
             #ncol=2
             )
FacetOBR10to25

Orders with Maximum Alpha Diversity > 100

FacetOBR25to100 <- ggplot(OBR25to100DF, aes(x=Biome, y=Alpha, fill=Biome, color=Biome)) + 
  geom_boxplot(show.legend = FALSE, fill=biome_cols_87, color="black", outlier.size=0.7) +
  #un-comment whichever theme you want
  #theme_minimal() +
  theme_gray() +
  #theme_light() +
  #theme_bw() +
  #theme_dark() +
  #theme_linedraw() +
  geom_violin(scale="count", show.legend=FALSE, fill="gray", alpha=0.35, color="gray25") +
  xlab("Biome") +
  ylab("Richness") +  
  theme(axis.title.y = element_text(size=32), 
        axis.title.x = element_text(size=32),
        axis.text.y = element_text(size=15), 
        axis.text.x = element_text(angle = 30, hjust = 1, size = 10)) +
  facet_wrap(~Order, 
             #un-comment # of rows you want
             ncol=4
             #ncol=2
             )
FacetOBR25to100

Circle Plots

Species richness for each order, grouped by biome

All bryophyte orders

FacetOBRAbove100 <- ggplot(OBRAbove100DF, aes(x=Biome, y=Alpha, fill=Biome, color=Biome)) + 
  geom_boxplot(show.legend = FALSE, fill=biome_cols_22, color="black",  outlier.size=1) +
  #un-comment whichever theme you want
  #theme_minimal() +
  theme_gray() +
  #theme_light() +
  #theme_bw() +
  #theme_dark() +
  #theme_linedraw() +
  geom_violin(scale="count", show.legend=FALSE, fill="gray", alpha=0.35, color="gray25") +
  xlab("Biome") +
  ylab("Richness") +  
  theme(axis.title.y = element_text(size=32), 
        axis.title.x = element_text(size=32),
        axis.text.y = element_text(size=15), 
        axis.text.x = element_text(angle = 45, hjust = 1, size = 12)) +
  facet_wrap(~Order, 
             #un-comment # of rows you want
             ncol=2
             #ncol=1
             )
FacetOBRAbove100

Only moss orders

circos.clear()
circos.par(start.degree = 0)
chordDiagram(CircleMatAll, grid.col = grid.col, column.col = biome_cols_11, 
             directional = 1, direction.type = "arrows", link.arr.type = "big.arrow", 
             link.arr.length = 0.05, link.largest.ontop = T, annotationTrack = c("grid"), 
             preAllocateTracks = 1, big.gap = 20, small.gap = 2)
circos.trackPlotRegion(track.index = 1, panel.fun = function(x, y) {
  xlim = get.cell.meta.data("xlim")
  ylim = get.cell.meta.data("ylim")
  sector.name = get.cell.meta.data("sector.index")
  circos.text(mean(xlim), ylim[1], sector.name, facing = "clockwise", niceFacing = TRUE, adj = c(0, 0.5), cex=0.5)
}, bg.border = NA)